Random thoughts and essays on life, religion, science, ethics, and social issues.

"Truth is so obscure in these times, and falsehood so established, that, unless we love the truth, we cannot know it." - Blaise Pascal

October 17, 2005

Abiogenesis: A Problem of Origins (part 1)

(Part 1 in a 3 part series)

If I were a creationist, I would cease attacking the theory of evolution - which is so well supported by the fossil record - and focus instead on the origin of life. This is by far the weakest strut of the chassis of modern biology. The origin of life is a science writer's dream. It abounds with exotic scientists and exotic theories, which are never entirely abandoned or accepted, but merely go in and out of fashion.Horgan, John [Senior Writer, Scientific American], The End of Science: Facing the Limits of Knowledge in the Twilight of the Scientific Age, New York: Broadway Books, 1996

Of all the issues that must be addressed by evolutionary theory, the problem of abiogenesis is the most fundamental and troublesome – it is the soft underbelly of evolutionary science. In fact, it is such a difficult issue that evolutionists are quick to separate it from the topic of evolution at large, where they feel they are on firmer ground. But without abiogenesis there is nothing to "evolve." It may be a separate question, but the failure to account for it is a logical defeater to the materialistic project in which evolution is so prominently featured.

So what exactly is abiogenesis? Well, for life to evolve it must first exist in some self-replicating form. And since prior to life there is only simple chemistry, there is a chasm that must be bridged. Life must somehow come from non-life: abiogenesis. Of course, this is not an issue if you are willing to accept that God has intervened in nature, but for scientists intent on finding a "natural" cause for life this has proved an intractable problem. Let me now step into the world of the naturalistic scientists to share some of their frustrations. Of course, to do so I must take on their assumption of an ancient earth, whether or not that is actually the case, but as we shall see it will be of little assistance.

The first problem that biochemists face is the vast complexity of the life that is to be explained. The earliest and oldest known life forms are very much like the single celled bacteria and algae that are still with us today. In Darwin's day, prior to refined optics and electron microscopes, such cells were perceived as mere blobs of "protoplasm." The development of, and evolutionary changes in, such a thing is far easier to imagine than what the cell actually turns out to be.

In reality, the cell is a marvel of biochemical machinery and information storage. As Bruce Alberts, president of the National Academy of Sciences, wrote in the biology journal Cell:

We have always underestimated cells. … The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. … Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts.

Biochemist Michael Denton, author of Evolution: A Theory in Crisis, adds another remarkable cellular feature when he writes, "it would be a factory which would have one capacity not equaled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours."

Such modern revelations about the cell have exceeded the limits of credulity for most evolutionary scientists. In the words of astronomer and physicist Sir Fred Hoyle, the probability of the spontaneous generation of a single bacterium "is about the same as the probability that a tornado sweeping through a junk yard could assemble a Boeing 747 from the contents therein." Francis Crick, co-discoverer of the DNA molecule, observed, "The origin of life appears to be almost a miracle, so many are the conditions which would have had to be satisfied to get it going." And our recognition of the complexity of the "simple cell" has only increased since these statements were made.

For this reason, it is not assumed that such organisms were the first in the chain of existence. It is then assumed that something less complex must have preceded the common single cell organism. Unfortunately, there is nothing simpler known or hinted at in the fossil record. As far back as we can examine there is life of this same kind, and before that there is only barren rock. It is no wonder that even secular presentations of this historical event use phrases like "a miracle occurred" to cover their loss of explanation.
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24 Comments:

Ah, and I know the problem is even worse than part 1 here describes it.Interesting then, how all school children are taught about the success of the Miller-Urey experiment that "created the building blocks of life in a lab."That's a blantant misuse of revisionist scientism for indoctrination.

I think that's a good point about how you can't have evolution without reproduction. So between chemistry and life, there could not have been evolution. The first living things could not have evolved.

But there is a possible defeater. When I studied chemistry in the navy, we learned about auto-catalytic reactions. Some chemical reactions feed on themselves. The products of the reaction act as a catalyst to keep the reaction going. Something like that could have provided some kind of "evolution" that lead to the first form of life.

Aren't viruses more simple forms of life than simple cells? I've heard that it's debatable whether viruses should even be considered "life," although they reproduce. Now granted, viruses depend for their survival on other cells. However, they nevertheless still show that it's possible for there to be more simple forms of life than cells. It could be that whatever existed prior to bacteria or whatever just hasn't survived in the fossil record. Perhaps because whatever there was, there wasn't much of it. It wasn't until it finally became bacteria that it really took off and spread.

Sam, it's actually much worse than you depict. If Paul doesn't cover it in parts 2 or 3, I'll add more details.I think what you describe from Chemistry is what would be called an exothermic reaction. It can be shown that these types of reactions are impossible in prebiotic conditions.

viruses cannot exist without hosts, so they must necessarily have come first. The simplest bacteria today have thousands of genes, even given the benefit of the doubt, that there might have been some minimalist bacteria in the beginning it would still have needed hundreds of genes just to support replication. This isn't possible without DNA and RNA in place first.

And beside that, there is fossil evidence of replicating microbial life right from 3.85 billion years ago. Right around the instant the earth's crust hardened. This makes it impossible to appeal to happenstance and long time periods for the chemical accident to have happened. Many scientists nowadays will admit that abiogenesis must happen automatically and quickly...deterministically. Otherwise there's no chance it would have happened, let alone instantly.

I've been surprised that I don't hear the origins of life researchers suggest the virus connection, but it seems understood that viruses came after the fact. They are both non-self-replicating and vulnerable to the elements outside of a protecting host. Even so, they are highly complex molecules with even worse chances of forming up than the "simplest" proteins. I'll probably discuss proteins in the next post (hope I don't regret wading into the science).

Speculation on this is fun, but we all have limited expertise here. What compels me so much about this issue is that very many scientists at the top of their fields, who are also not Christian (many are not even theists), have thrown their hands up over this issue. As far as I can tell, the theories we hear bandied about in the media or Discover Channel have been largely abandoned in the academy. When you work out the theoretical chemistry, you just don't come up with the necessary chemical pathways to create anything noteworthy. It's like stirring 1000 ball bearings in a kettle. It doesn't matter how long you do it, you'll never make an engine out of them. If dozens of atheists who are experts in this field want to tell me that it's just beyond their understanding, I'm not going to argue with them. In the area of evolution, I can take their own data and show they've come to the wrong conclusion, but in this issue they've done all the work for me. All that's left is for me to point out the situation.

One point of clarification. It seems that it's not even accurate to say that "it's just beyond their understanding". The fact is that chemistry is very well understood. I'm concerned that someone would read that to mean that we are using a God of the gaps argument. The truth of the matter is that chemistry is a hard science and the scientists know of no way within the laws of chemistry that life could have arisen.

That's why so many have gone the panspermia route. They claim that some imaginary world could have had conditions not even conceivable on earth and perhaps with elements not yet known to our periodic table. Then once life arose there, it could have been carried by solar winds on debris from an asteroid hit.Really that's about all the hope they have at this point.

I think you've overextended yourself with the "not yet known to our periodic table." The only potential elements left are high up the table, which means they would have a huge atomic mass, meaning they would be freak elements that would have to come about in exotic stellar environments. Plus, there would be little flexibility with such elements to work as molecular building blocks, like carbon does. Light molecules are the best and most abundant, and carbon is the absolute best core molecule. Perhaps a post on the problems of silicon (once proposed as an alternative) and the remarkable properties of carbon would be instructive.

You're right that they do understand chemistry pretty well, and that's what's such a problem for them. Those who say things like "life as we know it" are seeking to escape the constraints of chemistry with their imagination. But I see imagination employed constantly in the life of the materialist. In fact, I think I mention in my last post that evolutionists charge their skeptics with a "failure of imagination." We can certainly be gracious to the ignorance inherent in emerging science, but there are some issues that seem insurmountable in principle.

And exothermic reaction is not the same thing as an autocatalytic reaction. An exothermal reaction is a reaction that gives off heat. An autocatalytic reaction is a reaction whose products act as catalysts to keep the reaction going. I've been doing some reading tonight on autocatalytic reactions, and I found out that there are self-replicating molecules. There's a lot of research going on right now into self-replicating molecules as a possible explanation for how replication could've taken place before cells.

I grant that viruses can't exist without cells, but that misses my point. My point was only that it's possible for more simple forms of life to exist besides cells. Viruses may not be able to reproduce without cells, but maybe some other more simple form of life that we don't happen to know about could. The only way you could rule out the possibility is to argue that self-replication isn't possible without cells.

Question about autocatalytic reactions...Does it have any bearing? The question isn't whether chemistry works, the question is can chemistry result in biology?Wouldn't an autocatalytic reaction that's not happening in a lab, require an influx of energy to continue? (otherwise you violate the 2nd law of thermodynamics). And wouldn't a reaction that requires an influx of energy be called an endothermic reaction?

I know of no sequence of autocatalytic reactions that can proceed from simple compounds to more complex compounds in an unbroken cascade that finally results in amino acids or proteins.

The biological definition of 'life' is an organism that carries on the 5 basic metabolic activities: respiration, ingestion, digestion, excretion, reproduction.Viruses fail on a few of these grounds. Anything simpler than a cell probably can't do this. Now if we want to loosen up our definition of life to something that can replicate that's fine. But there will still be a boundary to cross between chemistry and biology.

Oh, and even though something like a virus couldn't survive and replicate, it also couldn't be arrived at via chemistry...you can't even get proteins via chemistry.

My point in bringing up autocatalytic reactions is to address Paul's point that before you can have evolution, you first have to have replication. Autocatalytic reactions are possible means of replication which could possibly result in more complex molecules.

Whether the reactions are exothermic or endothermic isn't relevent. The question is whether they replicate. Autocatalytic reactions don't violate the second law of thermodynamics. No chemical reaction in nature happens in a closed system. Energy can come from the sun, from other reactions, from the earth (magma, hot springs, etc.) and several other sources.

But having read more about it last night, I think self-replicating molecules are probably a better example than autocatalytic reactions.

I dont' know of any specific reactions that can produce proteins and such either. But if these reactions occure, then it seems at least possible that such a thing could happen. All you need for evolution is self-replication.

It's not relevent whether viruses are "life" or not. It's not relevent whether anything more simple than a cell is "life." What's relevent is whether self-replication can take place without cells. If it can, the it's possible that cellulare life could have evolved.

Sam, I disagree that autocatalytic reactions are all that's needed to say that cellular life could have evolved. I might even disagree with applying the term 'self-replicating' to an autocatalytic reaction. the simple fact that the reaction creates more catalyst guarantees that the chemical reaction will eventually end, and will end with more chemicals...not with biology.

The 2nd law still applies to earth, even though there is an influx of energy from the sun. I can dig up articles in support of that if you'd like.

Check out 'autocatalytic' on wikipedia. It states up front that the reaction needs an influx of energy or 'food' to continue.

I'm curious whether you are playing devil's advocate or whether you believe that science has a plausible answer for the origin of life question. If you actually believe that science has an answer, I think you'll be pleasantly surprised to find that they really don't.

Yes it's true that you first have to have reproduction before it can technically be termed evolution, but that wasn't my primary point. My point was to show that not only is a cell as complex as a factory, but it is even more complex in that it can marshal all its resources to make a copy of itself. It may be conceptually simple (maybe not in practice) to replicate a single molecule, but to replicate all the machinery of the cell, get it aligned, and then perform the division is a remarkable task.

Even if we can find a chemical pathway to come up with some self-replicating molecule you are still miles from any meaningful next step. This is a route that I see being proposed by some — the idea of intermediate molecules and proto-cells — but there is 1) no evidence for the pathways, 2) no good explanation for the how such pathways might proceed, and 3) great gaping chasms between each imagined step. At best, it is like imagining that we can get from Florida to South America by jumping from island to island.

I might disagree with calling autocatalytic reactions "self-replicating" too, but they are similar. Even so, there are molecules that are self-replicating. That shows that cells aren't necessary for self-replication.

Having studied physics and thermodynamics in both the navy and in college, I'm quite informed about the second law of thermodynamics.

All chemical reactions require "food." Otherwise, what's there to react? That includes the chemical reactions that go on in cell reproduction.

I think I said somewhere else on Paul's blog that I don't know enough about chemistry, biology, evolution, and intelligent design to have a strong opinion or to argue for any view. So I'm not trying to argue against your view so much as I'm trying to get answers to questions that came to my mind when I read Paul's post.

Paul, I guess I misunderstood your point. What kind of evidence would you expect there to be if there were intermediate steps before cells? It's hard for me to imagine what kind of evidence would've been left. The only reason we have any evidence of very early cells is because cells have membranes, and mebranes create texture, which can be preserved in rocks or whatever. But just chemical reactions happening in fluids wouldn't leave any traces, would they?

If cells are irreducibly complex, then I would have to agree that no process of evolution could produce them. But if not, then I don't see why it wouldn't at least be possible that self-replicating molecules could evolve in such a way that would eventually produce cells.

Sam, good honest questions. I think that you might be able to teach us something from your navy knowledge.

As for your last question to Paul: I think that there would be evidence. If there were a certain proposed intermediary step that theoretically consists of a large amount of a certain compound then there would be chemical evidence in sediment layed down at that time. Paleogeology is probably the name for that field of study.

Even if cells weren't irreducibly complex, I wouldn't automatically relinquish the point. That first jump from chemistry to biology must somehow explain the creation of a very complex single-celled organism that carries out respiration, ingestion, secretion, and reproduction via a DNA program...and it must have developed in a way that does NOT appeal to random mutation, and probably not to natural selection.

Having some background in these sciences I think you'd be extremely stimulated by some of the literature in this area. I can recommend a few great books if you're interested (ones written to a popular audience).

"What kind of evidence..." — I would expect to see chemical signatures for the kinds of molecules and protocells that are being suggested. I'd expect to see evidence for the kind of atmosphere and oceans that could create such a thing. I'd expect to see a workable model for how such molecules could be formed.

As I understand it, we do not merely find direct traces of microscopic life in the early geological layers, we also find the kinds of chemical byproducts that accompany such life, and these chemical signatures are missing in the layers beneath. These chemical traces were exactly what were being debated in the Mars rock controversy, i.e., was it Martian life, Martian life byproduct, a complex crystalline structure, or just contamination from Earth. Since the precursor protocells must be chemically similar, or at least chemically distinctive, we should find some chemical traces among the normal silicate and crystal structures of the strata. There is nothing.

I think there is a problem with even getting your first simple self-replicating molecule to occur by natural assembly — problems with the building blocks for such a thing as well as problems with assembling them into the necessary configuration.

Even so, at some point these molecules need to completely transform their function in order to cover the needs of the next step up the chain. There are some gaping holes in what could possible exist between such a self-replicator and the irreducibly complex "simple cell," which depends on such things as a protective cell wall, a protein manufacturing plant, an amino acid and energy supply chain, a protein instruction source, not to mention the logistics of moving things around, dealing with protein folding, waste management, replication, and event management.

As to whether it is theoretically possible to run the necessary chain of events to get to a bacteria, I'm inclined to say yes but I'm not sure if I can. There just doesn't seem to be a supply of the necessary chemicals to get started and there may be no legitimate pathways between the various points. This means that each step would need to be yet another miraculous and unique jump with the required chemicals and molecules to assemble that next step just magically arriving from somewhere. The only solution I can think of is if the preceding step always ended with a molecular machine that was capable of building not itself, but the next step up the ladder. This is like saying a robot magically appeared that could replicate itself, but then one day his software got scrambled which resulted in the instructions and inclination to build a super robot, and so on until you get a Godbot.

Paul, what you're saying about chemical evidence makes good sense. But how exhaustive can our search for the precursors to life possibly be? I mean the earth is a pretty big place, and if all life on earth has a common origin, then that origin must've been located in a small area. Looking for it would be like trying to find a needle in a haystack. It seems that we could only get a general idea of atmospheric conditions and local chemistry by examining sedimentary layers from various spots around the world. If the evidence for ancient chemistry were very strong, I would think there would be more of a consensus about what it was like. The diversity in opinion seems to suggest that we just don't know that much about the chemistry in those days. Our evidence isn't very exhaustive at all. We have a little evidence on which we can make general speculations, and that's about it. With the little evidence we have, I don't think we can rule out the possibility that some conditions existed somewhere that might've given rise to the necessary chemicals. That possibility would be good grounds for continuing the search. I don't think we could start ruling out the possibility until the search has been a little more exhaustive.

Sam, depending on your epistomological framework you will either decide that chemical evolution happened unless it's proven exhaustively it didn't or you will say that it should be proven possible and/or likely before you'll believe it.

That diversity of opinion you speak of exists precisely because of the naturalistic framework employed by these scientists that will never consider an intelligent agent in the origin. That's the sole reason you see diversity of opinion. And really the science against a prebiotic soup is very strong and settled (from my understanding).What you see is people arguing about what type of soup would be necessary for chemical evolution and then despite the evidence they will assume that type of soup existed.

But perhaps my strongest recommendation to you, because you've got the intellect to handle it, is: Mere Creation. It's edited by William Dembsky. Chapter 5 is written by Stephen C. Meyer and contains a fairly detailed discussion of the problems of abiogenesis. This book is the single best rundown I've seen of all of the scientific challenges faced by naturalism, as well as the positive evidence for ID. It gets scientifically detailed enough that it would be hard for the average person to understand all of it (yet no less valuable to them)...but I think that for you, it will be ideal.

I yanked this from a reader review on Amazon (for The Fifth Miracle); it's a quotation from Davies:

In claiming that water means life, NASA scientists are not merely being upbeat about their project. They are making--tacitly--a huge [italics] and profound assumption about the nature of nature. They are saying, in effect, that the laws of the universe are cunningly contrived to coax life into being against the raw odds; that the mathematical principles of physics, in their elegant simplicity, somehow know in advance about life and its vast complexity. If life follows from soup with causal dependability, the laws of nature encode a hidden subtext, a cosmic imperative, which tells them: 'Make life!' And, through life, its by-products: mind, knowledge, understanding. It means the laws of the universe have engineered their own comprehension. This is a breathtaking vision of nature, magnificent and uplifting in its majestic sweep. I hope it is correct. It would be wonderful if it were correct. But if it is, it represents a shift in the scientific world-view as profound as that initiated by Copernicus and Darwin put together. It should not be glossed over with glib statements that water plus organics equals life, obviously, for it is far from obvious (p. 246).

I thought this was interesting because either way, the theist comes out ahead. Either the teleological argument gets stronger yet, or the case for special creation does.

The problem with the needle in the haystack idea is that this means the volume of materials involved is dramatically reduced, and with it the odds of yielding anything. It is not as though if you get just the right chemicals together in the right place they will magically assemble into RNA and proteins. The great hope was that if we had entire oceans full of a rich broth of the chemicals, and we had plenty of time to work with, then "anything can happen." But great oceans and lakes leave traces, which are absent. Yet even were that the case, there are still logistical problems of assembling certain molecules in the presence of water and oxygen (which it appears existed on early earth).

The alternative to all this is to come up with some exotic and isolated environment that contains the right molecular precursors and has a clearly defined chemical pathway which would forgo the need of raw chance. Every model explored seems to lack all the required materials or a feasible pathway. We don't need to look for the needle (chemical evidence) in places where we know in principle it won't be. And no one's got a good idea where we ought to be looking for that evidence. There are known issues with deep sea hydrothermal vents, clay basin, cometary material, etc. All this is why "directed panspermia" (seeding by aliens) is a legitimate theory nowadays.

Paul, since Davies is way too friendly to naturalism, and doesn't have a background in chemistry, I think he's too friendly to the propaganda. I prefer something written by Shapiro on this subject. because he's a biochemist and at the top of the field of origin of life studies. Although I haven't read this...

I'm starting to remember why I gave up trying to learn about evolution and ID a few years ago. It's too complicated. Not that it's impossible to learn, but it sure does seem like it's going to take a lot to be proficient. Thanks for your recomendations and thoughts, though.